Sodium in PDB 8vu4: Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor

The structure of Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor, PDB code: 8vu4 was solved by A.U.Singer, H.A.Bruce, A.Pavlenco, L.Ploder, G.Luu, L.Blazer, J.J.Adams, S.S.Sidhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.40 / 2.35
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.863, 55.893, 87.016, 80.05, 89.91, 82.7
R / Rfree (%)	20.8 / 25.2

The structure of Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor (pdb code 8vu4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor, PDB code: 8vu4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in the Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:62.7 occ:1.00 O B:SER146 3.7 59.8 1.0 O G:HOH449 3.8 55.8 1.0 O B:GLY147 3.9 63.8 1.0 OG1 B:THR149 4.0 59.0 1.0 O G:HOH406 4.4 53.5 1.0 C B:GLY147 4.4 60.6 1.0 CB B:THR149 4.6 52.3 1.0 CA B:GLY147 4.7 57.2 1.0 C B:SER146 4.8 61.1 1.0 N B:THR149 4.9 58.9 1.0

Sodium binding site 2 out of 14 in the Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:56.2 occ:1.00 OE1 B:GLU162 2.4 36.3 0.7 OE2 B:GLU162 2.8 41.6 0.7 CD B:GLU162 2.8 39.3 0.7 N B:VAL164 3.2 38.7 1.0 CB B:PRO163 3.2 38.3 1.0 CA B:PRO163 3.3 40.5 1.0 O B:VAL164 3.5 36.8 1.0 C B:PRO163 3.8 40.4 1.0 OE1 B:GLU162 4.1 45.0 0.3 OH B:TYR159 4.1 43.7 1.0 CG B:GLU162 4.2 42.2 0.7 CG2 B:VAL164 4.2 37.7 1.0 CD B:GLU162 4.2 42.5 0.3 O B:HOH424 4.2 42.4 1.0 CA B:VAL164 4.3 33.1 1.0 C B:VAL164 4.3 40.8 1.0 CD2 B:LEU192 4.4 43.7 1.0 CG B:GLU162 4.5 42.1 0.3 CB B:GLU162 4.5 41.4 0.7 CB B:ALA182 4.5 43.2 1.0 O B:HOH422 4.5 37.5 1.0 CB B:GLU162 4.6 41.5 0.3 N B:PRO163 4.7 44.0 1.0 OE2 B:GLU162 4.7 37.5 0.3 CG B:PRO163 4.8 39.0 1.0 CB B:VAL164 4.9 33.9 1.0 CA B:GLU162 5.0 41.1 0.7 CA B:GLU162 5.0 41.1 0.3

Sodium binding site 3 out of 14 in the Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:48.5 occ:1.00 OH B:TYR103 2.7 54.1 1.0 O B:GLN120 3.0 53.7 1.0 CE1 B:TYR103 3.2 49.5 1.0 CZ B:TYR103 3.4 51.3 1.0 C C:LYS48 3.5 44.5 1.0 O C:GLY47 3.7 58.8 1.0 CA C:LYS48 3.7 46.0 1.0 N C:ALA49 3.7 48.7 1.0 N C:LYS48 3.7 49.8 1.0 C C:GLY47 3.8 50.7 1.0 O C:LYS48 3.8 42.1 1.0 C B:GLN120 4.1 52.2 1.0 CA C:ALA49 4.4 43.1 1.0 O B:HOH410 4.4 41.6 1.0 CD1 B:TYR103 4.5 46.1 1.0 CA C:GLY47 4.7 47.7 1.0 CG1 B:VAL101 4.7 38.8 1.0 CE2 B:TYR103 4.7 50.0 1.0 CA B:GLN120 4.8 50.5 1.0 CB C:ALA49 5.0 44.5 1.0

Sodium binding site 4 out of 14 in the Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:Na306 b:58.7 occ:1.00 CG C:GLN120 2.4 58.9 1.0 O C:MET4 2.8 62.0 1.0 NE2 C:GLN120 3.0 60.7 1.0 N C:GLN6 3.0 56.5 1.0 N C:GLN120 3.1 48.0 1.0 CD C:GLN120 3.1 68.8 1.0 CA C:THR5 3.3 58.1 1.0 C C:THR5 3.6 60.4 1.0 C C:MET4 3.7 66.3 1.0 CB C:GLN120 3.7 48.1 1.0 CA C:GLY119 3.7 49.9 1.0 N C:THR5 3.9 60.7 1.0 C C:GLY119 3.9 44.9 1.0 CB C:GLN6 4.0 53.6 1.0 CA C:GLN120 4.0 44.5 1.0 NZ G:LYS208 4.0 75.4 1.0 CA C:GLN6 4.1 55.5 1.0 OE1 C:GLN120 4.3 67.0 1.0 CB C:THR5 4.4 60.5 1.0 O C:GLN6 4.5 55.1 1.0 CG2 C:THR5 4.6 57.9 1.0 O G:HOH425 4.7 62.0 1.0 OG1 C:THR5 4.7 62.6 1.0 C C:GLN6 4.8 56.8 1.0 O C:THR5 4.9 61.7 1.0 O C:PHE118 5.0 48.2 1.0 N C:GLY119 5.0 47.8 1.0 CA C:MET4 5.0 62.7 1.0

Sodium binding site 5 out of 14 in the Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:Na307 b:57.3 occ:1.00 OG C:SER222 3.4 49.7 1.0 O C:THR220 4.0 53.0 1.0 CB C:SER222 4.4 40.6 1.0 C C:THR220 4.6 47.1 1.0 N C:SER222 4.6 42.6 1.0 C C:THR221 5.0 43.0 1.0

Sodium binding site 6 out of 14 in the Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:Na308 b:43.6 occ:1.00 O C:HOH448 2.0 50.9 1.0 OG1 C:THR200 2.6 43.3 1.0 O C:THR198 2.7 40.6 1.0 O C:HOH451 3.3 41.9 1.0 CB C:THR200 3.4 41.9 1.0 N C:THR200 3.5 35.9 1.0 C C:THR198 3.6 40.4 1.0 O C:ASN178 3.7 41.9 1.0 CA C:SER179 3.7 38.3 1.0 N C:GLN180 3.8 43.7 1.0 C C:SER179 4.0 43.5 1.0 C C:LEU199 4.0 36.2 1.0 CA C:THR200 4.1 39.5 1.0 OE1 C:GLN180 4.2 50.4 1.0 C C:ASN178 4.2 40.0 1.0 CA C:LEU199 4.2 34.6 1.0 N C:SER179 4.2 36.2 1.0 CG2 C:THR198 4.2 38.8 1.0 CB C:THR198 4.3 36.5 1.0 N C:LEU199 4.3 32.1 1.0 CG C:GLN180 4.4 48.5 1.0 O A:HOH433 4.4 38.5 1.0 O C:HOH406 4.4 49.6 1.0 O C:HOH404 4.5 43.6 1.0 CB C:GLN180 4.5 42.4 1.0 CA C:THR198 4.6 36.5 1.0 CG2 C:THR200 4.7 41.4 1.0 CA C:GLN180 4.7 43.2 1.0 CD C:GLN180 4.8 49.0 1.0 O C:LEU199 4.8 38.2 1.0 O C:SER179 4.8 42.5 1.0 CB C:SER179 4.9 37.4 1.0

Sodium binding site 7 out of 14 in the Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:Na309 b:54.7 occ:1.00 OD1 C:ASN172 3.6 64.2 1.0 CG C:TYR169 4.0 38.6 1.0 CD1 C:TYR169 4.0 43.9 1.0 CG2 C:THR224 4.2 35.6 1.0 CB C:TYR169 4.2 43.4 1.0 CD2 C:TYR169 4.4 39.5 1.0 CB C:ALA213 4.5 33.5 1.0 CE1 C:TYR169 4.5 42.8 1.0 OE2 C:GLU215 4.6 47.6 1.0 OG1 C:THR224 4.7 39.6 1.0 CG C:ASN172 4.8 62.4 1.0 CE2 C:TYR169 4.8 46.6 1.0 CZ C:TYR169 4.9 47.2 1.0

Sodium binding site 8 out of 14 in the Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:60.3 occ:1.00 O A:VAL126 2.5 44.4 1.0 O A:SER187 2.6 56.2 1.0 O A:HOH417 2.9 48.4 1.0 O A:HOH436 3.3 58.6 1.0 C A:VAL126 3.6 47.8 1.0 C A:SER187 3.7 51.8 1.0 CB A:ALA96 3.7 52.7 1.0 CA A:ALA96 3.8 52.1 1.0 OG1 A:THR99 4.0 45.7 1.0 ND2 A:ASN128 4.1 53.1 1.0 CA A:SER187 4.2 49.4 1.0 CB A:VAL126 4.2 53.3 1.0 O A:ALA96 4.3 52.7 1.0 O A:PHE127 4.3 51.1 1.0 C A:PHE127 4.4 52.1 1.0 CB A:SER187 4.4 52.8 1.0 CA A:VAL126 4.5 49.0 1.0 N A:PHE127 4.5 47.1 1.0 CA A:PHE127 4.5 49.9 1.0 C A:ALA96 4.6 52.4 1.0 N A:GLY188 4.7 50.1 1.0 CG1 A:VAL126 4.7 54.0 1.0 CG A:ASN128 4.8 53.9 1.0 N A:VAL126 4.9 45.2 1.0 N A:ALA96 5.0 53.1 1.0

Sodium binding site 9 out of 14 in the Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:48.7 occ:1.00 O C:HOH452 2.9 42.9 1.0 O A:PRO181 2.9 46.8 1.0 CA A:LEU192 3.3 37.0 1.0 CG1 A:VAL183 3.3 49.5 1.0 O A:SER191 3.4 40.8 1.0 CB C:SER182 3.6 37.7 1.0 CB A:LEU192 3.8 39.4 1.0 N A:VAL183 3.8 40.9 1.0 OG C:SER182 3.9 44.1 1.0 N A:SER193 4.0 33.2 1.0 C A:PRO181 4.0 37.9 1.0 O C:HOH424 4.0 44.0 1.0 O C:HOH431 4.0 43.4 1.0 CA A:ALA182 4.1 40.9 1.0 C A:LEU192 4.1 32.1 1.0 C A:SER191 4.1 37.8 1.0 C A:ALA182 4.2 40.6 1.0 CB A:PHE180 4.2 36.1 1.0 N A:LEU192 4.2 34.6 1.0 CB A:VAL183 4.3 45.2 1.0 CG2 A:VAL183 4.4 43.2 1.0 OG C:SER196 4.4 43.9 1.0 N A:ALA182 4.5 43.3 1.0 CA A:VAL183 4.7 43.4 1.0 C A:PHE180 4.9 34.2 1.0 O A:ALA182 5.0 42.7 1.0

Sodium binding site 10 out of 14 in the Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of FABS1CE4-Epr-1, An Elbow-Locked High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:44.5 occ:1.00 O A:PRO163 2.6 36.9 1.0 N A:LYS215 3.0 44.3 1.0 O A:ASN213 3.5 39.8 1.0 C A:PRO163 3.5 35.9 1.0 CA A:HIS214 3.6 40.9 1.0 CB A:LYS215 3.7 36.2 1.0 C A:HIS214 3.8 38.4 1.0 CA A:VAL164 3.8 38.3 1.0 CD A:PRO216 3.9 40.9 1.0 CA A:LYS215 3.9 44.2 1.0 C A:ASN213 4.0 38.5 1.0 CG A:PRO163 4.0 40.5 1.0 N A:VAL164 4.1 38.3 1.0 N A:HIS214 4.1 32.2 1.0 CD A:PRO163 4.2 38.7 1.0 C A:VAL164 4.3 39.6 1.0 ND2 A:ASN213 4.4 55.4 1.0 N A:THR165 4.4 36.5 1.0 CA A:PRO163 4.5 36.7 1.0 CB A:PRO163 4.6 36.2 1.0 CG A:LYS215 4.8 39.1 1.0 CD2 A:HIS214 4.8 35.4 1.0 N A:PRO216 4.8 44.8 1.0 N A:PRO163 4.8 42.2 1.0 C A:LYS215 4.9 44.6 1.0 CB A:HIS214 4.9 39.5 1.0 OG1 A:THR165 4.9 37.4 1.0 CG2 A:THR165 4.9 31.0 1.0 O A:HIS214 5.0 45.0 1.0 CG A:ASN213 5.0 54.3 1.0

H.A.Bruce, A.U.Singer, L.L.Blazer, K.Luu, L.Ploder, A.Pavlenco, I.Kurinov, J.J.Adams, S.S.Sidhu. Antigen-Binding Fragments with Improved Crystal Lattice Packing and Enhanced Conformational Flexibility at the Elbow Region As Crystallization Chaperones. Protein Sci. V. 33 E5081 2024.
ISSN: ESSN 1469-896X
PubMed: 38924648
DOI: 10.1002/PRO.5081